1
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Hartman JD, Capistran D. Predicting 51V nuclear magnetic resonance observables in molecular crystals. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:416-428. [PMID: 38114304 DOI: 10.1002/mrc.5420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy and quantum chemical density functional theory (DFT) calculations are widely used to characterize vanadium centers in biological and pharmaceutically relevant compounds. Several techniques have been recently developed to improve the accuracy of predicted NMR parameters obtained from DFT. Fragment-based and planewave-corrected methods employing hybrid density functionals are particularly effective tools for solid-state applications. A recent benchmark study involving molecular crystal compounds found that fragment-based NMR calculations using hybrid density functionals improve the accuracy of predicted 51V chemical shieldings by 20% relative to traditional planewave methods. This work extends the previous study, including a careful analysis of 51V chemical shift anisotropy, electric field gradient calculations, and a more extensive test set. The accuracy of planewave-corrected techniques and recently developed fragment-based methods using electrostatic embedding based on the polarized continuum model (PCM) are found to be highly competitive with previous methods. Planewave-corrected methods achieve a 34% improvement in the errors of predicted 51V chemical shieldings relative to planewave. Additionally, planewave-corrected and fragment-based calculations were performed using PCM embedding, improving the accuracy of predicted 51V chemical shielding (CS) tensor principal values by 30% andC q values by 15% relative to traditional planewave methods. The performance of these methods is further examined using a redox-active oxovandium complex and a common 51V NMR reference compound.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Daniel Capistran
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
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2
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Chaloupecká E, Tyrpekl V, Bártová K, Nishiyama Y, Dračínský M. NMR crystallography of amino acids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 130:101921. [PMID: 38422809 DOI: 10.1016/j.ssnmr.2024.101921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.
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Affiliation(s)
- Ema Chaloupecká
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Václav Tyrpekl
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic
| | | | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic.
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3
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Holmes ST, Boley CM, Dewicki A, Gardner ZT, Vojvodin CS, Iuliucci RJ, Schurko RW. Carbon-13 chemical shift tensor measurements for nitrogen-dense compounds. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:179-189. [PMID: 38230444 DOI: 10.1002/mrc.5422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
This paper reports the principal values of the 13 C chemical shift tensors for five nitrogen-dense compounds (i.e., cytosine, uracil, imidazole, guanidine hydrochloride, and aminoguanidine hydrochloride). Although these are all fundamentally important compounds, the majority do not have 13 C chemical shift tensors reported in the literature. The chemical shift tensors are obtained from 1 H→13 C cross-polarization magic-angle spinning (CP/MAS) experiments that were conducted at a high field of 18.8 T to suppress the effects of 14 N-13 C residual dipolar coupling. Quantum chemical calculations using density functional theory are used to obtain the 13 C magnetic shielding tensors for these compounds. The best agreement with experiment arises from calculations using the hybrid functional PBE0 or the double-hybrid functional PBE0-DH, along with the triple-zeta basis sets TZ2P or pc-3, respectively, and intermolecular effects modeled using large clusters of molecules with electrostatic embedding through the COSMO approach. These measurements are part of an ongoing effort to expand the catalog of accurate 13 C chemical shift tensor measurements, with the aim of creating a database that may be useful for benchmarking the accuracy of quantum chemical calculations, developing nuclear magnetic resonance (NMR) crystallography protocols, or aiding in applications involving machine learning or data mining. This work was conducted at the National High Magnetic Field Laboratory as part of a 2-week school for introducing undergraduate students to practical laboratory experience that will prepare them for scientific careers or postgraduate studies.
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Affiliation(s)
- Sean T Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - Cameron M Boley
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Angelika Dewicki
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Zachary T Gardner
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Cameron S Vojvodin
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - Robbie J Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Robert W Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
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4
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Widdifield CM, Zakeri F. Can simple 'molecular' corrections outperform projector augmented-wave density functional theory in the prediction of 35 Cl electric field gradient tensor parameters for chlorine-containing crystalline systems? MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:156-168. [PMID: 37950622 DOI: 10.1002/mrc.5408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/13/2023]
Abstract
Many-body expansion (MBE) fragment approaches have been applied to accurately compute nuclear magnetic resonance (NMR) parameters in crystalline systems. Recent examples demonstrate that electric field gradient (EFG) tensor parameters can be accurately calculated for 14 N and 17 O. A key additional development is the simple molecular correction (SMC) approach, which uses two one-body fragment (i.e., isolated molecule) calculations to adjust NMR parameter values established using 'benchmark' projector augmented-wave (PAW) density functional theory (DFT) values. Here, we apply a SMC using the hybrid PBE0 exchange-correlation (XC) functional to see if this can improve the accuracy of calculated 35 Cl EFG tensor parameters. We selected eight organic and two inorganic crystal structures and considered 15 chlorine sites. We find that this SMC improves the accuracy of computed values for both the 35 Cl quadrupolar coupling constant (CQ ) and the asymmetry parameter ( η Q ) by approximately 30% compared with benchmark PAW DFT values. We also assessed a SMC that offers local improvements not only in terms of the quality of the XC functional but simultaneously in the quality of the description of relativistic effects via the inclusion of spin-orbit effects. As the inorganic systems considered contain heavy atoms bonded to the chlorine atoms, we find further improvements in the accuracy of calculated 35 Cl EFG tensor parameters when both a hybrid functional and spin-orbit effects are included in the SMC. On the contrary, for chlorine-containing organics, the inclusion of spin-orbit relativistic effects using a SMC does not improve the accuracy of computed 35 Cl EFG tensor parameters.
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Affiliation(s)
- Cory M Widdifield
- Department of Chemistry and Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Fatemeh Zakeri
- Department of Chemistry and Biochemistry, University of Regina, Regina, Saskatchewan, Canada
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5
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Beran GJO. Frontiers of molecular crystal structure prediction for pharmaceuticals and functional organic materials. Chem Sci 2023; 14:13290-13312. [PMID: 38033897 PMCID: PMC10685338 DOI: 10.1039/d3sc03903j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
The reliability of organic molecular crystal structure prediction has improved tremendously in recent years. Crystal structure predictions for small, mostly rigid molecules are quickly becoming routine. Structure predictions for larger, highly flexible molecules are more challenging, but their crystal structures can also now be predicted with increasing rates of success. These advances are ushering in a new era where crystal structure prediction drives the experimental discovery of new solid forms. After briefly discussing the computational methods that enable successful crystal structure prediction, this perspective presents case studies from the literature that demonstrate how state-of-the-art crystal structure prediction can transform how scientists approach problems involving the organic solid state. Applications to pharmaceuticals, porous organic materials, photomechanical crystals, organic semi-conductors, and nuclear magnetic resonance crystallography are included. Finally, efforts to improve our understanding of which predicted crystal structures can actually be produced experimentally and other outstanding challenges are discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
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6
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Hartman JD, Spock LE, Harper JK. Benchmark accuracy of predicted NMR observables for quadrupolar 14 N and 17 O nuclei in molecular crystals. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:253-267. [PMID: 36567433 DOI: 10.1002/mrc.5328] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Nuclear quadrupole resonances for 14 N and 17 O nuclei are exquisitely sensitive to interactions with surrounding atoms. As a result, nitrogen and oxygen solid-state nuclear magnetic resonance (ssNMR) provides a powerful tool for investigating structure and dynamics in complex systems. First-principles calculations are increasingly used to facilitate spectral assignment and to evaluate and adjust crystal structures. Recent work combining the strengths of planewave density functional theory (DFT) calculations with a single molecule correction obtained using a higher level of theory has proven successful in improving the accuracy of predicted chemical shielding (CS) tensors and 17 O quadrupolar coupling constants ( C q ). Here we extend this work by examining the accuracy of predicted 14 N and 17 O electric field gradient (EFG) tensor components obtained using alternative planewave-corrections involving cluster and two-body fragment-based calculations. We benchmark the accuracy of CS and EFG tensor predictions for both nitrogen and oxygen using planewave, two-body fragment, and enhanced planewave-corrected techniques. Combining planewave and two-body fragment calculations reduces the error in predicted 17 O C q values by 35% relative to traditional planewave calculations. These enhanced planewave-correction methods improve the accuracy of 17 O and 14 N EFG tensor components by 15% relative to planewave DFT but yield minimal improvement relative to a simple molecular correction. However, in structural environments involving either high symmetry or strong intermolecular interactions, enhanced planewave-corrected methods provide a distinct advantage.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Lilian E Spock
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
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7
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Iuliucci RJ, Hartman JD, Beran GJO. Do Models beyond Hybrid Density Functionals Increase the Agreement with Experiment for Predicted NMR Chemical Shifts or Electric Field Gradient Tensors in Organic Solids? J Phys Chem A 2023; 127:2846-2858. [PMID: 36940431 DOI: 10.1021/acs.jpca.2c07657] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Ab initio predictions of chemical shifts and electric field gradient (EFG) tensor components are frequently used to help interpret solid-state nuclear magnetic resonance (NMR) experiments. Typically, these predictions employ density functional theory (DFT) with generalized gradient approximation (GGA) functionals, though hybrid functionals have been shown to improve accuracy relative to experiment. Here, the performance of a dozen models beyond the GGA approximation are examined for the prediction of solid-state NMR observables, including meta-GGA, hybrid, and double-hybrid density functionals and second-order Møller-Plesset perturbation theory (MP2). These models are tested on organic molecular crystal data sets containing 169 experimental 13C and 15N chemical shifts and 114 17O and 14N EFG tensor components. To make these calculations affordable, gauge-including projector augmented wave (GIPAW) Perdew-Burke-Ernzerhof (PBE) calculations with periodic boundary conditions are combined with a local intramolecular correction computed at the higher level of theory. Within the context of typical NMR property calculations performed on a static, DFT-optimized crystal structure, the benchmarking finds that the double-hybrid DFT functionals produce errors versus experiment that are no smaller than those of hybrid functionals in the best cases, and they can be larger. MP2 errors versus experiment are even bigger. Overall, no practical advantages are found for using any of the tested double-hybrid functionals or MP2 to predict experimental solid-state NMR chemical shifts and EFG tensor components for routine organic crystals, especially given the higher computational cost of those methods. This finding likely reflects error cancellation benefiting the hybrid functionals. Improving the accuracy of the predicted chemical shifts and EFG tensors relative to experiment would probably require more robust treatments of the crystal structures, their dynamics, and other factors.
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Affiliation(s)
- Robbie J Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301 United States
| | - Joshua D Hartman
- Department of Chemistry, University of California, Riverside, California 92521 United States
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521 United States
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8
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Hartman JD, Harper JK. Improving the accuracy of GIPAW chemical shielding calculations with cluster and fragment corrections. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101832. [PMID: 36198253 DOI: 10.1016/j.ssnmr.2022.101832] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Ab initio methods for predicting NMR parameters in the solid state are an essential tool for assigning experimental spectra and play an increasingly important role in structural characterizations. Recently, a molecular correction (MC) technique has been developed which combines the strengths of plane-wave methods (GIPAW) with single molecule calculations employing Gaussian basis sets. The GIPAW + MC method relies on a periodic calculation performed at a lower level of theory to model the crystalline environment. The GIPAW result is then corrected using a single molecule calculation performed at a higher level of theory. The success of the GIPAW + MC method in predicting a range of NMR parameters is a result of the highly local character of the tensors underlying the NMR observable. However, in applications involving strong intermolecular interactions we find that expanding the region treated at the higher level of theory more accurately captures local many-body contributions to the N15 NMR chemical shielding (CS) tensor. We propose alternative corrections to GIPAW which capture interactions between adjacent molecules at a higher level of theory using either fragment or cluster-based calculations. Benchmark calculations performed on N15 and C13 data sets show that these advanced GIPAW-corrected calculations improve the accuracy of chemical shielding tensor predictions relative to existing methods. Specifically, cluster-based N15 corrections show a 24% and 17% reduction in RMS error relative to GIPAW and GIPAW + MC calculations, respectively. Comparing the benchmark data sets using multiple computational models demonstrates that N15 CS tensor calculations are significantly more sensitive to intermolecular interactions relative to C13. However, fragment and cluster-based corrections that include direct hydrogen bond partners are sufficient for optimizing the accuracy of GIPAW-corrected methods. Finally, GIPAW-corrected methods are applied to the particularly challenging NMR spectral assignment of guanosine dihydrate which contains two guanosine molecules in the asymmetric unit.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States.
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, United States.
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9
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Blahut J, Štoček JR, Šála M, Dračínský M. The hydrogen bond continuum in solid isonicotinic acid. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 345:107334. [PMID: 36410062 DOI: 10.1016/j.jmr.2022.107334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The understanding and correct description of intermolecular hydrogen bonds are crucial in the field of multicomponent pharmaceutical solids, such as salts and cocrystals. Solid isonicotinic acid can serve as a suitable model for the development of methods that can accurately characterize these hydrogen bonds. Experimental solid-state NMR has revealed a remarkable temperature dependence and deuterium-isotope-induced changes of the chemical shifts of the atoms involved in the intermolecular hydrogen bond; these NMR data are related to changes of the average position of the hydrogen atom. These changes of NMR parameters were interpreted using periodic DFT path-integral molecular dynamics (PIMD) simulations. The small size of the unit cell of isonicotinic acid allowed for PIMD simulations with the computationally demanding hybrid DFT functional. Calculations of NMR parameters based on the hybrid-functional PIMD simulations are in excellent agreement with experiment. It is thus demonstrated that an accurate characterization of intermolecular hydrogen bonds can be achieved by a combination of NMR experiments and advanced computations.
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Affiliation(s)
- Jan Blahut
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Jakub Radek Štoček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, 128 40 Prague 2, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic.
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10
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Cordova M, Engel EA, Stefaniuk A, Paruzzo F, Hofstetter A, Ceriotti M, Emsley L. A Machine Learning Model of Chemical Shifts for Chemically and Structurally Diverse Molecular Solids. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:16710-16720. [PMID: 36237276 PMCID: PMC9549463 DOI: 10.1021/acs.jpcc.2c03854] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Nuclear magnetic resonance (NMR) chemical shifts are a direct probe of local atomic environments and can be used to determine the structure of solid materials. However, the substantial computational cost required to predict accurate chemical shifts is a key bottleneck for NMR crystallography. We recently introduced ShiftML, a machine-learning model of chemical shifts in molecular solids, trained on minimum-energy geometries of materials composed of C, H, N, O, and S that provides rapid chemical shift predictions with density functional theory (DFT) accuracy. Here, we extend the capabilities of ShiftML to predict chemical shifts for both finite temperature structures and more chemically diverse compounds, while retaining the same speed and accuracy. For a benchmark set of 13 molecular solids, we find a root-mean-squared error of 0.47 ppm with respect to experiment for 1H shift predictions (compared to 0.35 ppm for explicit DFT calculations), while reducing the computational cost by over four orders of magnitude.
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Affiliation(s)
- Manuel Cordova
- Laboratory
of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- National
Centre for Computational Design and Discovery of Novel Materials MARVEL, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Edgar A. Engel
- Theory
of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Artur Stefaniuk
- Laboratory
of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Federico Paruzzo
- Laboratory
of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Albert Hofstetter
- Laboratory
of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Michele Ceriotti
- National
Centre for Computational Design and Discovery of Novel Materials MARVEL, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Laboratory
of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Lyndon Emsley
- Laboratory
of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- National
Centre for Computational Design and Discovery of Novel Materials MARVEL, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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11
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Abadian H, Cornette P, Costa D, Mezzetti A, Gervais C, Lambert JF. Leucine on Silica: A Combined Experimental and Modeling Study of a System Relevant for Origins of Life, and the Role of Water Coadsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8038-8053. [PMID: 35737817 DOI: 10.1021/acs.langmuir.2c00841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Leucine on silica constitutes an interesting system from the point of view of origins of life studies since leucine coadsorbed on SiO2 together with glutamic acid can give rise to rather long linear polypeptides upon activation. It is also an ideal system to test methods of molecular characterization of biomolecules deposited on mineral surfaces since it combines a small-scale model of peptides and proteins, which are among the most important components of biodevices, with one of the most widely used inorganic materials. We have deposited l-leucine on a high surface fumed silica in the submonolayer range and characterized it by a multipronged approach including macroscopic information (thermogravimetry, X-ray diffraction), in situ spectroscopic methods (IR, multinuclear solid-state NMR including single-pulse and CP-MAS, 2-D HETCOR), and molecular modeling by density functional theory (DFT), including calculation of NMR parameters. Specific information can be obtained on the adsorption and interaction mechanism. Leucine is rather strongly adsorbed without any covalent bonds, through the formation of a specific lattice of H-bonds that often involve coadsorbed water molecules. Its state is indeed strongly dependent on the drying procedure: insufficient drying results in liquid-like surroundings for the leucine functional groups, while vacuum drying only retains a limited number of waters (of the order of 5 per leucine molecule). The most stable models have zwitterionic leucine interacting directly with surface silanols through their ammonium group, while the carboxylate interacts through bridging waters. Experimental NMR chemical shifts are satisfactorily predicted for these models, and leucine can be viewed as a probe for specific groups of surface sites known as silanol nests.
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Affiliation(s)
- Hagop Abadian
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP, UMR 7574 CNRS), Case courrier 174, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Pauline Cornette
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Dominique Costa
- Institut de Recherche de Chimie Paris (IRCP, UMR8247 CNRS), 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alberto Mezzetti
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP, UMR 7574 CNRS), Case courrier 174, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
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12
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Poidevin C, Stoychev GL, Riplinger C, Auer AA. High Level Electronic Structure Calculation of Molecular Solid-State NMR Shielding Constants. J Chem Theory Comput 2022; 18:2408-2417. [PMID: 35353527 PMCID: PMC9009078 DOI: 10.1021/acs.jctc.1c01095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In this work, we
present a quantum mechanics/molecular mechanics
(QM/MM) approach for the computation of solid-state nuclear magnetic
resonance (SS-NMR) shielding constants (SCs) for molecular crystals.
Besides applying standard-DFT functionals like GGAs (PBE), meta-GGAs
(TPSS), and hybrids (B3LYP), we apply a double-hybrid (DSD-PBEP86)
functional as well as MP2, using the domain-based local pair natural
orbital (DLPNO) formalism, to calculate the NMR SCs of six amino acid
crystals. All the electronic structure methods used exhibit good correlation
of the NMR shieldings with respect to experimental chemical shifts
for both 1H and 13C. We also find that local
electronic structure is much more important than the long-range electrostatic
effects for these systems, implying that cluster approaches using
all-electron/Gaussian basis set methods might offer great potential
for predictive computations of solid-state NMR parameters for organic
solids.
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Affiliation(s)
- Corentin Poidevin
- Institut des Sciences Chimiques de Rennes, Av. Général Leclerc, 357000 Rennes, France
| | - Georgi L Stoychev
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | | | - Alexander A Auer
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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13
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Han J, Kang H, Kang S, Kwon Y, Lee D, Choi YS. Scalable graph neural network for NMR chemical shift prediction. Phys Chem Chem Phys 2022; 24:26870-26878. [DOI: 10.1039/d2cp04542g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a scalable graph neural network (GNN) with improved message passing and readout functions for the fast and accurate prediction of nuclear magnetic resonance (NMR) chemical shifts.
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Affiliation(s)
- Jongmin Han
- Department of Industrial Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Hyungu Kang
- Department of Industrial Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Seokho Kang
- Department of Industrial Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Youngchun Kwon
- Samsung Advanced Institute of Technology, Samsung Electronics Co. Ltd., Yeongtong-gu, Suwon 16678, Republic of Korea
- Department of Computer Science and Engineering, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Dongseon Lee
- Samsung Advanced Institute of Technology, Samsung Electronics Co. Ltd., Yeongtong-gu, Suwon 16678, Republic of Korea
| | - Youn-Suk Choi
- Samsung Advanced Institute of Technology, Samsung Electronics Co. Ltd., Yeongtong-gu, Suwon 16678, Republic of Korea
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14
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Hartman JD, Mathews A, Harper JK. Fast and Accurate Electric Field Gradient Calculations in Molecular Solids With Density Functional Theory. Front Chem 2021; 9:751711. [PMID: 34692646 PMCID: PMC8529703 DOI: 10.3389/fchem.2021.751711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022] Open
Abstract
Modern approaches for calculating electric field gradient (EFF) tensors in molecular solids rely upon plane-wave calculations employing periodic boundary conditions (PBC). In practice, models employing PBCs are limited to generalized gradient approximation (GGA) density functionals. Hybrid density functionals applied in the context of gauge-including atomic orbital (GIAO) calculations have been shown to substantially improve the accuracy of predicted NMR parameters. Here we propose an efficient method that effectively combines the benefits of both periodic calculations and single-molecule techniques for predicting electric field gradient tensors in molecular solids. Periodic calculations using plane-wave basis sets were used to model the crystalline environment. We then introduce a molecular correction to the periodic result obtained from a single-molecule calculation performed with a hybrid density functional. Single-molecule calculations performed using hybrid density functionals were found to significantly improve the agreement of predicted 17O quadrupolar coupling constants (C q ) with experiment. We demonstrate a 31% reduction in the RMS error for the predicted 17O C q values relative to standard plane-wave methods using a carefully constructed test set comprised of 22 oxygen-containing molecular crystals. We show comparable improvements in accuracy using five different hybrid density functionals and find predicted C q values to be relatively insensitive to the choice of basis set used in the single molecule calculation. Finally, the utility of high-accuracy 17O C q predictions is demonstrated by examining the disordered 4-Nitrobenzaldehyde crystal structure.
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Affiliation(s)
- Joshua D. Hartman
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, United States
| | - Amanda Mathews
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, United States
| | - James K. Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, United States
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15
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Engel EA, Kapil V, Ceriotti M. Importance of Nuclear Quantum Effects for NMR Crystallography. J Phys Chem Lett 2021; 12:7701-7707. [PMID: 34355903 DOI: 10.1021/acs.jpclett.1c01987] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of computational predictions of NMR chemical shieldings of candidate structures, which are usually taken to be local minima in the potential energy. To test the limits of this approximation, we systematically study the importance of finite-temperature and quantum nuclear fluctuations for 1H, 13C, and 15N shieldings in polymorphs of three paradigmatic molecular crystals: benzene, glycine, and succinic acid. The effect of quantum fluctuations is comparable to the typical errors of shielding predictions for static nuclei with respect to experiments, and their inclusion improves the agreement with measurements, translating to more reliable assignment of the NMR spectra to the correct candidate structure. The use of integrated machine-learning models, trained on first-principles energies and shieldings, renders rigorous sampling of nuclear fluctuations affordable, setting a new standard for the calculations underlying NMR structure determinations.
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Affiliation(s)
- Edgar A Engel
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Venkat Kapil
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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16
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Mathews A, Hartman JD. Accurate fragment-based 51-V chemical shift predictions in molecular crystals. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 114:101733. [PMID: 34082261 DOI: 10.1016/j.ssnmr.2021.101733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy plays a crucial role in determining molecular structure for complex biological and pharmaceutical compounds. NMR investigations are increasingly reliant on computation for mapping spectral features to chemical structures. Here we benchmark the accuracy of fragment-based 51V chemical shielding tensor calculations using a training set comprised of 10 biologically and pharmaceutically relevant oxovanadium complexes. Using our self-consistent reproduction of the Madelung potential (SCRMP) electrostatic embedding model, we demonstrate comparable performance between fragment methods and computationally demanding cluster-based techniques. Specifically, fragment methods employing hybrid density functionals are capable of reproducing the experimental 51V isotropic chemical shifts with a training set rms error of ~9 ppm, representing a 20% improvement over traditional plane wave techniques. We provide training set-derived linear regression models for mapping the absolute shieldings obtained from computation to the experimentally determined chemical shifts using four common density functionals; PBE0, B3LYP, PBE, and BLYP. Finally, we establish the utility of fragment methods and the reported regression parameters examining four oxovanadium structures excluded from the training set including the tetracoordinate oxovanadium silicate [Formula: see text] , VO15NGlySalbz which contains redox-active ligands, and the solid-state form of the common 51V NMR reference compound VOCl3.
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Affiliation(s)
- Amanda Mathews
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, USA
| | - Joshua D Hartman
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, USA.
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17
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Duong NT, Aoyama Y, Kawamoto K, Yamazaki T, Nishiyama Y. Structure Solution of Nano-Crystalline Small Molecules Using MicroED and Solid-State NMR Dipolar-Based Experiments. Molecules 2021; 26:molecules26154652. [PMID: 34361806 PMCID: PMC8347922 DOI: 10.3390/molecules26154652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided that kinetic analysis is used. Consequently, there remains ambiguity to locate hydrogens and to assign nuclei with close atomic numbers, like carbon, nitrogen, and oxygen. Herein, we employed microED and ssNMR dipolar-based experiments together with spin dynamics numerical simulations. The NMR dipolar-based experiments were 1H-14N phase-modulated rotational-echo saturation-pulse double-resonance (PM-S-RESPDOR) and 1H-1H selective recoupling of proton (SERP) experiments. The former examined the dephasing effect of a specific 1H resonance under multiple 1H-14N dipolar couplings. The latter examined the selective polarization transfer between a 1H-1H pair. The structure was solved by microED and then validated by evaluating the agreement between experimental and calculated dipolar-based NMR results. As the measurements were performed on 1H and 14N, the method can be employed for natural abundance samples. Furthermore, the whole validation procedure was conducted at 293 K unlike widely used chemical shift calculation at 0 K using the GIPAW method. This combined method was demonstrated on monoclinic l-histidine.
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Affiliation(s)
- Nghia Tuan Duong
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
| | | | | | - Toshio Yamazaki
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
- JEOL RESONANCE Inc., Akishima, Tokyo 196-8558, Japan
- Correspondence:
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18
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Analyzing Discrepancies in Chemical-Shift Predictions of Solid Pyridinium Fumarates. Molecules 2021; 26:molecules26133857. [PMID: 34202841 PMCID: PMC8270278 DOI: 10.3390/molecules26133857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 01/29/2023] Open
Abstract
Highly accurate chemical-shift predictions in molecular solids are behind the success and rapid development of NMR crystallography. However, unusually large errors of predicted hydrogen and carbon chemical shifts are sometimes reported. An understanding of these deviations is crucial for the reliability of NMR crystallography. Here, recently reported large deviations of predicted hydrogen and carbon chemical shifts of a series of solid pyridinium fumarates are thoroughly analyzed. The influence of the geometry optimization protocol and of the computational level of NMR calculations on the accuracy of predicted chemical shifts is investigated. Periodic calculations with GGA, meta-GGA and hybrid functionals are employed. Furthermore, molecular corrections at the coupled-cluster singles-and-doubles (CCSD) level are calculated. The effect of nuclear delocalization on the structure and NMR shielding is also investigated. The geometry optimization with a computationally demanding hybrid functional leads to a substantial improvement in proton chemical-shift predictions.
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19
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Pem B, Toma M, Vrček V, Vinković Vrček I. Combined NMR and Computational Study of Cysteine Oxidation during Nucleation of Metallic Clusters in Biological Systems. Inorg Chem 2021; 60:4144-4161. [PMID: 33657797 DOI: 10.1021/acs.inorgchem.1c00321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The widespread biomedical applications of silver and gold nanoparticles (AgNPs and AuNPs, respectively) prompt the need for mechanistic evaluation of their interaction with biomolecules. In biological media, metallic NPs are known to transform by various pathways, especially in the presence of thiols. The interplay between metallic NPs and thiols may lead to unpredictable consequences for the health status of an organism. This study explored the potential events occurring during biotransformation, dissolution, and reformation of NPs in the thiol-rich biological media. The study employed a model system evaluating the interaction of cysteine with small-sized AgNPs and AuNPs. The interplay of cysteine on transformation and reformation pathways of these NPs was experimentally investigated by nuclear magnetic resonance (NMR) spectroscopy and supported by light scattering techniques and transmission electron microscopy (TEM). As the main outcome, Ag- or Au-catalyzed oxidation of cysteine to cystine was found to occur through generation of reactive oxygen species (ROS). Computational simulations confirmed this mechanism and the role of ROS in the oxidative dimerization of biothiol during NPs reformation. The obtained results represent valuable mechanistic data about the complex events during the transport of metallic NPs in thiol-rich biological systems that should be considered for the future biomedical applications of metal-based nanomaterials.
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Affiliation(s)
- Barbara Pem
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Mateja Toma
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Valerije Vrček
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Ivana Vinković Vrček
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10000 Zagreb, Croatia
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20
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Shi M, Jin X, Wan Z, He X. Automated fragmentation quantum mechanical calculation of 13C and 1H chemical shifts in molecular crystals. J Chem Phys 2021; 154:064502. [PMID: 33588539 DOI: 10.1063/5.0039115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach was applied to calculate the 13C and 1H nuclear magnetic resonance (NMR) chemical shifts in molecular crystals. Two benchmark sets of molecular crystals were selected to calculate the NMR chemical shifts. Systematic investigation was conducted to examine the convergence of AF-QM/MM calculations and the impact of various density functionals with different basis sets on the NMR chemical shift prediction. The result demonstrates that the calculated NMR chemical shifts are close to convergence when the distance threshold for the QM region is larger than 3.5 Å. For 13C chemical shift calculations, the mPW1PW91 functional is the best density functional among the functionals chosen in this study (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB98, and OPBE), while the OB98 functional is more suitable for the 1H NMR chemical shift prediction of molecular crystals. Moreover, with the B3LYP functional, at least a triple-ζ basis set should be utilized to accurately reproduce the experimental 13C and 1H chemical shifts. The employment of diffuse basis functions will further improve the accuracy for 13C chemical shift calculations, but not for the 1H chemical shift prediction. We further proposed a fragmentation scheme of dividing the central molecule into smaller fragments. By comparing with the results of the fragmentation scheme using the entire central molecule as the core region, the AF-QM/MM calculations with the fragmented central molecule can not only achieve accurate results but also reduce the computational cost. Therefore, the AF-QM/MM approach is capable of predicting the 13C and 1H NMR chemical shifts for molecular crystals accurately and effectively, and could be utilized for dealing with more complex periodic systems such as macromolecular polymers and biomacromolecules. The AF-QM/MM program for molecular crystals is available at https://github.com/shiman1995/NMR.
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Affiliation(s)
- Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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21
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Unzueta PA, Greenwell CS, Beran GJO. Predicting Density Functional Theory-Quality Nuclear Magnetic Resonance Chemical Shifts via Δ-Machine Learning. J Chem Theory Comput 2021; 17:826-840. [DOI: 10.1021/acs.jctc.0c00979] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pablo A. Unzueta
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Chandler S. Greenwell
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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22
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Gately TJ, Sontising W, Easley CJ, Islam I, Al-Kaysi RO, Beran GJO, Bardeen CJ. Effect of halogen substitution on energies and dynamics of reversible photomechanical crystals based on 9-anthracenecarboxylic acid. CrystEngComm 2021. [DOI: 10.1039/d1ce00846c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A combined experimental/computational analysis of photomechanical anthracene derivatives reveals their kinetic behavior is not simply related to the monomer-photodimer energetics.
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Affiliation(s)
- Thomas J. Gately
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Watit Sontising
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Connor J. Easley
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Imadul Islam
- College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, and, King Abdullah International Medical Research Center (Nanomedicine), Ministry of National Guard Health Affairs, Riyadh 11426, Kingdom of Saudi Arabia
| | - Rabih O. Al-Kaysi
- College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, and, King Abdullah International Medical Research Center (Nanomedicine), Ministry of National Guard Health Affairs, Riyadh 11426, Kingdom of Saudi Arabia
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
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23
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Dittmer A, Stoychev GL, Maganas D, Auer AA, Neese F. Computation of NMR Shielding Constants for Solids Using an Embedded Cluster Approach with DFT, Double-Hybrid DFT, and MP2. J Chem Theory Comput 2020; 16:6950-6967. [PMID: 32966067 PMCID: PMC7659039 DOI: 10.1021/acs.jctc.0c00067] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In
this work, we explore the accuracy of post-Hartree–Fock
(HF) methods and double-hybrid density functional theory (DFT) for
the computation of solid-state NMR chemical shifts. We apply an embedded
cluster approach and investigate the convergence with cluster size
and embedding for a series of inorganic solids with long-range electrostatic
interactions. In a systematic study, we discuss the cluster design,
the embedding procedure, and basis set convergence using gauge-including
atomic orbital (GIAO) NMR calculations at the DFT and MP2 levels of
theory. We demonstrate that the accuracy obtained for the prediction
of NMR chemical shifts, which can be achieved for molecular systems,
can be carried over to solid systems. An appropriate embedded cluster
approach allows one to apply methods beyond standard DFT even for
systems for which long-range electrostatic effects are important. We find that an embedded
cluster should include at least one sphere of explicit neighbors around
the nuclei of interest, given that a sufficiently large point charge
and boundary effective potential embedding is applied. Using the pcSseg-3
basis set and GIAOs for the computation of nuclear shielding constants,
accuracies of 1.6 ppm for 7Li, 1.5 ppm for 23Na, and 5.1 ppm for 39K as well as 9.3 ppm for 19F, 6.5 ppm for 35Cl, 7.4 ppm for 79Br, and
7.5 ppm for 25Mg as well as 3.8 ppm for 67Zn
can be achieved with MP2. Comparing various DFT functionals with HF
and MP2, we report the superior quality of results for methods that
include post-HF correlation like MP2 and double-hybrid DFT.
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Affiliation(s)
- Anneke Dittmer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Georgi L Stoychev
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios Maganas
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Alexander A Auer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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24
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Dračínský M, Vícha J, Bártová K, Hodgkinson P. Towards Accurate Predictions of Proton NMR Spectroscopic Parameters in Molecular Solids. Chemphyschem 2020; 21:2075-2083. [PMID: 32691463 DOI: 10.1002/cphc.202000629] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/20/2020] [Indexed: 12/18/2022]
Abstract
The factors contributing to the accuracy of quantum-chemical calculations for the prediction of proton NMR chemical shifts in molecular solids are systematically investigated. Proton chemical shifts of six solid amino acids with hydrogen atoms in various bonding environments (CH, CH2 , CH3 , OH, SH and NH3 ) were determined experimentally using ultra-fast magic-angle spinning and proton-detected 2D NMR experiments. The standard DFT method commonly used for the calculations of NMR parameters of solids is shown to provide chemical shifts that deviate from experiment by up to 1.5 ppm. The effects of the computational level (hybrid DFT functional, coupled-cluster calculation, inclusion of relativistic spin-orbit coupling) are thoroughly discussed. The effect of molecular dynamics and nuclear quantum effects are investigated using path-integral molecular dynamics (PIMD) simulations. It is demonstrated that the accuracy of the calculated proton chemical shifts is significantly better when these effects are included in the calculations.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic
| | - Jan Vícha
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic.,Centre of Polymer Systems, Tomas Bata University in Zlín, Tomáše Bati 5678, Zlín, CZ-760 01, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, Prague, CZ-16610, Czech Republic
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, South Road, DH1 3LE, Durham, UK
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25
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Unzueta PA, Beran GJO. Polarizable continuum models provide an effective electrostatic embedding model for fragment-based chemical shift prediction in challenging systems. J Comput Chem 2020; 41:2251-2265. [PMID: 32748418 DOI: 10.1002/jcc.26388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/04/2020] [Accepted: 07/04/2020] [Indexed: 12/25/2022]
Abstract
Ab initio nuclear magnetic resonance chemical shift prediction provides an important tool for interpreting and assigning experimental spectra, but it becomes computationally prohibitive in large systems. The computational costs can be reduced considerably by fragmentation of the large system into a series of contributions from many smaller subsystems. However, the presence of charged functional groups and the need to partition the system across covalent bonds create complications in biomolecules that typically require the use of large fragments and careful descriptions of the electrostatic environment. The present work shows how a model that combines chemical shielding contributions from non-overlapping monomer and dimer fragments embedded in a polarizable continuum model provides a simple, easy-to-implement, and computationally inexpensive approach for predicting chemical shifts in complex systems. The model's performance proves rather insensitive to the continuum dielectric constant, making the selection of the optimal embedding dielectric less critical. The PCM-embedded fragment model is demonstrated to perform well across systems ranging from molecular crystals to proteins.
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Affiliation(s)
- Pablo A Unzueta
- Department of Chemistry, Univeristy of California, Riverside, California, USA
| | - Gregory J O Beran
- Department of Chemistry, Univeristy of California, Riverside, California, USA
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26
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Corlett EK, Blade H, Hughes LP, Sidebottom PJ, Walker D, Walton RI, Brown SP. Investigating discrepancies between experimental solid-state NMR and GIPAW calculation: NC-N 13C and OH⋯O 1H chemical shifts in pyridinium fumarates and their cocrystals. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 108:101662. [PMID: 32590237 DOI: 10.1016/j.ssnmr.2020.101662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
An NMR crystallography analysis is presented for four solid-state structures of pyridine fumarates and their cocrystals, using crystal structures deposited in the Cambridge Crystallographic Data Centre, CCDC. Experimental one-dimensional one-pulse 1H and 13C cross-polarisation (CP) magic-angle spinning (MAS) nuclear magnetic resonance (NMR) and two-dimensional 14N-1H heteronuclear multiple-quantum coherence MAS NMR spectra are compared with gauge-including projector augmented wave (GIPAW) calculations of the 1H and 13C chemical shifts and the 14N shifts that additionally depend on the quadrupolar interaction. Considering the high ppm (>10 ppm) 1H resonances, while there is good agreement (within 0.4 ppm) between experiment and GIPAW calculation for the hydrogen-bonded NH moieties, the hydrogen-bonded fumaric acid OH resonances are 1.2-1.9 ppm higher in GIPAW calculation as compared to experiment. For the cocrystals of a salt and a salt formed by 2-amino-5-methylpyridinium and 2-amino-6-methylpyridinium ions, a large discrepancy of 4.2 and 5.9 ppm between experiment and GIPAW calculation is observed for the quaternary ring carbon 13C resonance that is directly bonded to two nitrogens (in the ring and in the amino group). By comparison, there is excellent agreement (within 0.2 ppm) for the quaternary ring carbon 13C resonance directly bonded to the ring nitrogen for the salt and cocrystal of a salt formed by 2,6-lutidinium and 2,5-lutidinium, respectively.
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Affiliation(s)
- Emily K Corlett
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Helen Blade
- Pharmaceutical Development, AstraZeneca, Macclesfield, SK10 2NA, UK
| | - Leslie P Hughes
- Pharmaceutical Development, AstraZeneca, Macclesfield, SK10 2NA, UK
| | - Philip J Sidebottom
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - David Walker
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard I Walton
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.
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27
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Vícha J, Švec P, Růžičková Z, Samsonov MA, Bártová K, Růžička A, Straka M, Dračínský M. Experimental and Theoretical Evidence of Spin‐Orbit Heavy Atom on the Light Atom
1
H NMR Chemical Shifts Induced through H⋅⋅⋅I
−
Hydrogen Bond. Chemistry 2020; 26:8698-8702. [DOI: 10.1002/chem.202001532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Jan Vícha
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
- Centre of Polymer SystemsTomas Bata University in Zlín Tomáše Bati 5678 Zlín 760 01 Czech Republic
| | - Petr Švec
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Maksim A. Samsonov
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
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Holmes ST, Engl OG, Srnec MN, Madura JD, Quiñones R, Harper JK, Schurko RW, Iuliucci RJ. Chemical Shift Tensors of Cimetidine Form A Modeled with Density Functional Theory Calculations: Implications for NMR Crystallography. J Phys Chem A 2020; 124:3109-3119. [DOI: 10.1021/acs.jpca.0c00421] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Olivia G. Engl
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, United States
| | - Matthew N. Srnec
- Department of Chemistry, Physics, & Engineering, Franciscan University, Steubenville, Ohio 43952, United States
| | - Jeffry D. Madura
- Department of Chemistry & Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Rosalynn Quiñones
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - James K. Harper
- Department of Chemistry & Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Robert W. Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Robbie J. Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, United States
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Martel L, Kovács A, Popa K, Bregiroux D, Charpentier T. 31P MAS NMR and DFT study of crystalline phosphate matrices. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 105:101638. [PMID: 31810014 DOI: 10.1016/j.ssnmr.2019.101638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
We present the study of the phosphorus local environment by using 31P MAS NMR in a series of seven double monophosphates MIIMIV(PO4)2 (MII and MIV being divalent and tetravalent cations, respectively) of yavapaiite and low-yavapaiite type crystal structures. Solid-state and cluster DFT calculations were found to be efficient for predicting the 31P isotropic chemical shift and chemical shift anisotropy. To achieve this performance, however, a proper computational optimisation of the experimental structural data was required. From the three optimisation methods tested, the full optimisation provided the best reference structure for the calculation of the NMR parameters of the studied phosphates. Also, a better prediction of the chemical shifts was possible by using a correction to the GIPAW calculated shielding.
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Affiliation(s)
- Laura Martel
- European Commission, Joint Research Centre (JRC), Postfach 2340, D-76125, Karlsruhe, Germany.
| | - Attila Kovács
- European Commission, Joint Research Centre (JRC), Postfach 2340, D-76125, Karlsruhe, Germany
| | - Karin Popa
- European Commission, Joint Research Centre (JRC), Postfach 2340, D-76125, Karlsruhe, Germany
| | - Damien Bregiroux
- Sorbonne Université, CNRS, Chimie de la Matière Condensée de Paris, LCMCP, F-75005, Paris, France
| | - Thibault Charpentier
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
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Engel EA, Anelli A, Hofstetter A, Paruzzo F, Emsley L, Ceriotti M. A Bayesian approach to NMR crystal structure determination. Phys Chem Chem Phys 2019; 21:23385-23400. [PMID: 31631196 DOI: 10.1039/c9cp04489b] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is particularly well suited to determine the structure of molecules and materials in powdered form. Structure determination usually proceeds by finding the best match between experimentally observed NMR chemical shifts and those of candidate structures. Chemical shifts for the candidate configurations have traditionally been computed by electronic-structure methods, and more recently predicted by machine learning. However, the reliability of the determination depends on the errors in the predicted shifts. Here we propose a Bayesian framework for determining the confidence in the identification of the experimental crystal structure, based on knowledge of the typical errors in the electronic structure methods. We demonstrate the approach on the determination of the structures of six organic molecular crystals. We critically assess the reliability of the structure determinations, facilitated by the introduction of a visualization of the similarity between candidate configurations in terms of their chemical shifts and their structures. We also show that the commonly used values for the errors in calculated 13C shifts are underestimated, and that more accurate, self-consistently determined uncertainties make it possible to use 13C shifts to improve the accuracy of structure determinations. Finally, we extend the recently-developed ShiftML model to render it more efficient, accurate, and, most importantly, to evaluate the uncertainties in its predictions. By quantifying the confidence in structure determinations based on ShiftML predictions we further substantiate that it provides a valid replacement for first-principles calculations in NMR crystallography.
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Affiliation(s)
- Edgar A Engel
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
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31
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McKinley JL, Beran GJO. Improving Predicted Nuclear Magnetic Resonance Chemical Shifts Using the Quasi-Harmonic Approximation. J Chem Theory Comput 2019; 15:5259-5274. [PMID: 31442040 DOI: 10.1021/acs.jctc.9b00481] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ab initio nuclear magnetic resonance chemical shift prediction plays an important role in the determination or validation of crystal structures. The ability to predict chemical shifts more accurately can translate to increased confidence in the resulting chemical shift or structural assignments. Standard electronic structure predictions for molecular crystal structures neglect thermal expansion, which can lead to an appreciable underestimation of the molar volumes. This study examines this volume error and its impact on 68 13C- and 28 15N-predicted chemical shifts taken from 20 molecular crystals. It assesses the ability to recover more realistic room-temperature crystal structures using the quasi-harmonic approximation and how refining the structures impacts the chemical shifts. Several pharmaceutical molecular crystals are also examined in more detail. On the whole, accounting for quasi-harmonic expansion changes the 13C and 15N chemical shifts by 0.5 and 1.0 ppm on average. This, in turn, reduces the root-mean-square errors relative to experiment by 0.3 ppm for 13C and 0.7 ppm for 15N. Although the statistical impacts are modest, changes in individual chemical shifts can reach multiple ppm. Accounting for thermal expansion in molecular crystal chemical shift prediction may not be needed routinely, but the systematic trend toward improved accuracy with the experiment could be useful in cases where discrimination between structural candidates is challenging, as in the pharmaceutical theophylline.
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Affiliation(s)
- Jessica L McKinley
- Department of Chemistry , University of California , Riverside , California 92521 , United States
| | - Gregory J O Beran
- Department of Chemistry , University of California , Riverside , California 92521 , United States
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